Reloading a new clip into weapon "not working" is tied to whether of not the inventory space holding the extra magazines is at capacity. If the magazine you want to load is in an inventory slot that is full or at capacity (such as pants) you can not reload the weapon in hand by just pressing the Y button even if you have extra open inventory space in another area on your character (such as a back pack).
When my inventory space holding the extra magazine such as my pants is full, if I try to reload my weapon in hand by pressing the Y button only while in main character screen (not in inventory menu) it will not reload unless I go into the inventory menu while holding gun in hands, then I micromanage to the magazine in my hands and press Y on magazine to remove it. Then I have to highlight the full magazine in the inventory space and hit B to combine then it reloads.
However, if my inventory space holding the magazine is well below the maximum capacity, I can reload simply by pressing Y button while weapon is in my hands while in main game HUD (not in inventory mode).